Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/functions_comp2annottests.R
This function tests if the groups of samples formed by
the variables are differently distributed on the
components, in terms of contribution value (i.e of values
in matrix A(icaSet)
). The distribution of the
samples on the components are represented using either
density plots of boxplots. It is possible to restrict the
tests and the plots to a subset of samples and/or
components.
1 2 3 4 5 6 7 8 9  qualVarAnalysis(params, icaSet, keepVar,
keepComp = indComp(icaSet),
keepSamples = sampleNames(icaSet),
adjustBy = c("none", "component", "variable"),
method = "BH", doPlot = TRUE, typePlot = "density",
addPoints = FALSE, onlySign = TRUE,
cutoff = params["pvalCutoff"],
colours = annot2col(params), path = "qualVarAnalysis/",
filename = "qualVar", typeImage = "png")

params 
An object of class

icaSet 
An object of class

keepVar 
The variable labels to be considered, must
be a subset of 
keepComp 
A subset of components, must be included
in 
keepSamples 
A subset of samples, must be included
in 
adjustBy 
The way the pvalues of the Wilcoxon and
KruskalWallis tests should be corrected for multiple
testing: 
method 
The correction method, see

doPlot 
If TRUE (default), the plots are done, else only tests are performed. 
addPoints 
If TRUE, points are superimposed on the boxplot. 
typePlot 
The type of plot, either 
onlySign 
If TRUE (default), only the significant results are plotted. 
cutoff 
A threshold pvalue for statistical significance. 
colours 
A vector of colours indexed by the
variable levels, if missing the colours are automatically
generated using 
path 
A directory _within resPath(params)_ where
the files containing the plots and the pvalue results
will be located. Default is 
typeImage 
The type of image file to be used. 
filename 
The name of the HTML file containing the pvalues of the tests, if NULL no file is created. 
This function writes an HTML file containing the results
of the tests as a an array of dimensions 'variables *
components' containing the pvalues of the tests. When a
pvalue is considered as significant according to the
threshold cutoff
, it is written in bold and filled
with a link pointing to the corresponding plot. One image
is created by plot and located into the subdirectory
"plots/" of path
. Each image is named by
indexofcomponent_var.png. Wilcoxon or KruskalWallis
tests are performed depending on the number of groups of
interest in the considered variable (argument
keepLev
).
Returns A data.frame of dimensions 'components x variables' containing the pvalues of the nonparametric tests (Wilcoxon or KruskalWallis tests) wich test if the samples groups defined by each variable are differently distributed on the components.
Anne Biton
, qualVarAnalysis
, p.adjust
,
link{writeHtmlResTestsByAnnot}
,
wilcox.test
, kruskal.test
1 2 3 4 5 6 7 8 9 10 11 12 13 14  ## load an example of IcaSet
data(icaSetCarbayo)
## build MineICAParams object
params < buildMineICAParams(resPath="carbayo/")
## Define the directory containing the results
dir < paste(resPath(params), "comp2annot/", sep="")
## Run tests, make no adjustment of the pvalues,
# for variable grade and components 1 and 2,
# and plot boxplots when 'doPlot=TRUE'.
qualVarAnalysis(params=params, icaSet=icaSetCarbayo, adjustBy="none", typePlot="boxplot",
keepVar="GRADE", keepComp=1:2, path=dir, doPlot=FALSE)

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